In silico characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) based on the spike protein gene

Warghane, A and Petkar, T and Usha Preeyaa, S and Kumari, N and Ranjan, L (2021) In silico characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) based on the spike protein gene. In: Eurasian Journal of Medicine and Oncology, 5 (2). pp. 163-180.

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Abstract

Objectives: The Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 has been the current global pandemic concern. With a high transmission rate, especially through direct contact, this disease spreads from person to person, and this has in turn led to a huge number of infections on a global scale. Methods: In present study, comparative genomic analysis was performed using 151 gene sequences of the viral spike protein retrieved from NCBI and along with its translated nucleotide sequences using MEGAX software. Variation in the nucleotide and amino acid positions were identified. Results: Our analysis revealed that 22 nucleotide variations observed in positions 13, 141, 162, 233, 284, 328, 455, 459, 716, 773, 784, 882, 1686, 1715, 1749, 1841, 2031, 2076, 2383, 2520, 2533, 3300 and 17 amino acid variations observed in position 5, 54, 78, 90, 95, 152, 153, 239, 258, 262, 572, 583, 614, 684, 677, 795 and 845. Further, phylogenetic analysis was used to uncover the patterns of spread of the virus across the affected countries. Although, certain strains showed patterns of transmission within communities, a vast majority revealed an evident mosaic pattern. Conclusion: The data obtained provides a clear understanding of variations in the nucleotide and translated nucleotide sequences, which can be targeted towards drug designing and to study evolutionary analysis. © 2021 by Eurasian Journal of Medicine and Oncology.

Item Type:	Journal Article
Publication:	Eurasian Journal of Medicine and Oncology
Publisher:	Kare Publishing
Additional Information:	The copyright for this article belongs to Authors
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	26 Nov 2021 11:38
Last Modified:	26 Nov 2021 11:38
URI:	http://eprints.iisc.ac.in/id/eprint/70453

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